Turn of the Tides
by Sky14
Summary: Set between Matrix and Matrix reloaded PG-13 just in case.complete.
1. Default Chapter

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Turn of the tides 

Neo walks along the bridge of Zion near the docking area. He yells over the alarms. " What's going on?"

One of the crewmembers near him replies. " Sentinals. Hundreds of them are approaching.." He gets cut off as another yells. " They breached the hall! Get the EMP's!" 

Neo runs off to head off the sentinals. As they approach he sends blue energy towards them only this time he doesn't collapse. Before the last Sentinal goes down it grabs him charges with the blue energy. He collapses onto the deck.

People in hover over him in the hospital wing to try and determine what is wrong with him. After many hours some of them find something and at once go off to tell Morpheus. 

Trinity sits at Neo's bedside on a chair. She grips his hand tightly. She looks up as Morpheus walks into the room. She stands up and notices his grim face. " What is it Morpheus?"

He takes her aside and says. " We knows what's wrong with him."

" What is it?" She asks slowly.

" The Sentinal that grabbed him injected some sort of virus into his system. They do not know yet what it will do to his system. They have decided for some reason unknown reason to me that he shouldn't be told."

Tears threaten to spill down Trinity's face as she looks over at the now awake Neo. She composes herself as she walks over to him and sits back down in the chair. She takes his hand and offers him a weak smile.

He smiles at her. " Hey Trinity."

" How are you feeling Neo?" She looks at him with piercing eyes.

" I'm okay. How is everyone else?"

A tear threatens to fall and she quickly wipes it away. " Everyone is fine, and thanks to you the Sentinals were destroyed."

He nods. " Good."

She offers him another smile as she brushes a hand through his hair. " You should get some rest Neo. We are at peace for the moment." 

He nods and closes his eyes.

" How is he doing?" Morpheus asks quietly as he walks back in concern is evident in his voice. 

" He seems to be doing okay. He is sleeping at the moment. What do you think it will do to him Morpheus?" 

Morpheus sighs sadly. " I don't know Trinity. I wish I had some answers on this. The prophecies..."

Trinity cuts him off. " Is that all you care about is him being the one? There is so much more to him than that Morpheus. He many do amazing things here and in the Matrix but he is still human."

A few weeks later Neo is let out of the hospital wing. He walks down the bridges still unaware that anything was wrong with him. He walks into the Neb. were the rest of the crew is talking. Trinity looks up as he enters in shock and smiles at him as he walks up to her and gives her a kiss. " Hey Trinity."

The crewmembers smile at him and clap him on the back as the meeting is let out.

" Hey Neo. How are you feeling?" Trinity asks him.

He gives an exasperated sigh wishing people would stop asking that. " I'm fine how are you?" 

" I'm fine." She is about to say something but Neo asks. " What was that meeting about Trin?"

She smiles and shakes her head not wanting him to know. " It wasn't important just some last minute conversations before we take you to see the oracle again." 

He raises an eyebrow at her in confusion but says nothing more to her on the matter. " All right." He says as they head off to enter the matrix. 

As they sit in the chairs waiting to be downloaded into the Matrix Trinity tells Neo. " Stay close to us."

Neo sighs as they enter the Matrix. Agents swarm them as they step out onto the streets.

Neo's face turns pale and he doubles over as Agents rush him.

" Neo!" 

Neo grimaces as they agents tackle him down to the ground.

" We need an exit now!" Trinity yells into her phone. 

" Nearest exit is on the other side of town. It's an old apartment building room 629 on the 6th floor." Tank replied

" All right." She hangs up her phone. 

Morpheus stands over Neo's chair in the ship as it shakes violently. " Come on." He says quietly to Neo and Trinity.

Something drives the agents away and they leave Neo on the ground. 

One of the other people there picks up Neo and carries him to the phone. They force him to leave and they shortly join him.

They leave him in the chair afraid to move him as Trinity stands off to the side of him while he gets looked over.

He wakes with a start and Trinity puts a hand on his arm. " You need to relax Neo. They are trying to help you."

He wakes up a few hours later in a bed and glances around the room. 

" What happened in there Neo? We need to know." 

He looks up at the person that spoke and answers. " It felt like my whole body was on fire with such intense pain, and then the agents showed up and..."

Trinity takes his hand and says softly. " Come on Neo they need to know."

He takes a deep breath and continues. " They tried to make me into one of them again with some sort of new method and something happened that I am assuming they didn't expect." He lifts up his shirt to show them a massive nasty green bruise that covers his stomach.

Trinity, Morpheus, and the medical people there exchange dark looks at one another.

Neo notices this and looks at them. " What's going on here?"

" Nothing we just need you to stay out of the Matrix for a while." One of the doctors replies. 

He mutters under his breath. " Fine keep your secrets."

Trinity grips his hand tightly. " Neo please..." she pleads him. 

He sighs. " Fine can you tell me why at least?" He looks at her pleadingly. 

She looks up at the Doctors and they nod grimly. One stays in the room and the rest leave with Morpheus. 

She looks back at Neo and takes a deep breath before she begins. " Neo... During The last sentinal attack you held them at bay and destroyed them. But the last Sentinal injected some sort of virus into your system. We don't know exactly what it will do, but after your visit in the matrix we have some guesses..."

He shakes his head. " No. No it's not true. It can't be." He stands up quickly from the bed. " No!" 

" Neo you need to calm down... would I lie about something like this?" Trinity asks with tears streaming down her face.

He collapses onto the bed suddenly feeling sick he lunges for the garbage can and throws up. 

Trinity rubs his back as a doctor comes over and gives him a shot to relax and calm him down. The doctor helps him back into the bed and walks away. 

Neo lies there with his eyes closed for a moment not saying anything. 

" Neo..?" Trinity finally asks with her voice full of concern and worry.

He looks at her his face pale and void of emotion.

" Neo please say something.."

" Now I remember why I don't believe in fate." He says simply in a dull voice. " Life seems to be going somewhat normal, or as normal as it can around here. Then something like this happens and changes a persons life, but it's not just their life it's thousands of other people as well that are affected by this..." 

She stands up and moves from the chair and sits on his bed and hugs him. " Neo.. you need to think positive. Everything will work out. Get some rest all right? I'll be back in a little while."

He sighs as she leaves. He closes his eyes, but sleep is a long way off. 

Trinity walks outside along one of the bridges in search of Morpheus. 

" Trinity... how did he take the news?" Morpheus asks her.

" He is in denial about the whole thing.. What is it Morpheus?"

" We have to leave Zion. We need to go into the Matrix and find the oracle before they do."

" What about Neo?"

Morpheus sighs knowing she won't like the answer. " He has to come with us Trinity." He shakes his head sadly. " There isn't much choice in the matter. We leave when he wakes up again." 

A few hours later Neo wakes up feeling better. He looks around the room and sees Morpheus standing there. 

" Neo its time to leave."

Neo nods and a few minutes later he enters the room again ready to go. He walks along the bridges and enters the Neb. 

"Tank lets go." Morpheus says. 

Morpheus, Trinity, and Neo enter the Matrix. Neo hides a grimace of pain as intense blinding pain floods through his body. They near the last post the oracle was known to be.

There is a blinding flash of light and when the two of them look Neo is gone.

" Tank what happened?" Trinity asks.

" Something has him. He is being moved somewhere..." Tank answers. 

They exit the matrix and Trinity stands over Neo's chair. His chair shakes violently. " What are they doing to him Tank?" She asks.

************************************************************************

They drop him off in a room with a window that overlooks a lake. 

Neo sits in a chair staring out at the lake. His body in agony and numb from the pain. 

" Mr. Anderson. We meet again." Smith says as he forces Neo to look at him as a sheet of metal drops down and covers the window.

" What do you want?" Neo asks. 

" It's fairly simple Mr. Anderson. We ant you dead." Smith says in an almost bored tone. 

" What did the sentinal do to me?" Neo demands suddenly. 

Smith smiles. " You'll know in time." With that Smith leaves the room. 

************************************************************************

" We have to go in and save him.."

" Trinity we don't know what is holding him.."

She gives him a look that would kill him in less than a second if looks could kill. " Are you forgetting how he risked his life to save yours?!" 

Morpheus sighs. " I didn't forget, but we have to plan this out first."

Trinity sighs helplessly and wipes Neo's sweaty face with a wet cloth and wishes there was something that she could do for him. " Fine what do we do? Do we know where he is being held?"

Tank nods. " He is near ' Canada' in an old Military base."

************************************************************************

Neo sits in the corner of the room as Smith comes into the room and walks out shortly after. Neo desperately tries to think of a plan and get his mind to work past the pain that it registers. After a while he gives up and just stares blankly at the wall.

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Trinity looks down at Neo's body and wipes his sweaty face before she decides to take matters into her own hands and gets downloaded in the Matrix near the building Neo is held in. " Hang in there Neo.." She says quietly as she walks into the unguarded building. She glances around and realizes they left him here alone because they know he can't escape. She runs up the building stairs and eventually finds the room he is in and runs to him. ' Oh my God' she thinks ' what did they do to him?' She looks at him as she kneels next to him. " Neo..." she smiles in relief when she sees that he is still breathing. She drags him down the streets and leaves the Matrix after he does.

Morpheus helps her bring him down to the medical area.

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A few weeks later Neo wakes up. Through the shades that have been placed on his face he glances around. He notices Trinity and weakly squeezes her hand.

Trinity looks over at him and smiles brightly at him. " Neo.."

He turns his head towards her and says in a quiet horse voice. " Trinity..."

" Shh.. its all right you need to rest Neo." She runs a hand through his hair until he falls asleep. She gets up and walks outside and stands next to Morpheus who is talking to one of the doctors.

"... So you see it was a near fatal thing even for him. He needs to stay here in Zion and in the medical bay until he gets his strength back."

" Neo isn't going to allow that. He always puts others before himself, and that's what he will do here in Zion." Trinity says as she enters the conversation.

Morpheus nods in agreement. " She is right. There has to be another alternative to this Doctor."

The doctor shakes his head. " I'm sorry it's the only way. So we can keep an eye on him in a safe environment." The doctor says as he walks away.

Morpheus looks at Trinity. " Don't worry about it. Go be with him we can stay and wait. His health is the most important thing right now."

Trinity nods gratefully to Morpheus and walks back into the room Neo is in. She sits down in a chair next to his bedside.

Neo looks at her as she sits back down, and for a moment he says nothing pretending he is still asleep. He takes her hand. " I love you Trinity. Remember that no matter what may happen in the future.." He tells her quietly. 

" I know I love you too Neo."

Suddenly red and blue lights start to flash and alarms blare. 

Neo looks at Trinity as something clinks on the bridge outside the door...

**********************************************************************

" The tides have changed..." Smith says to the twins.

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Neo looks at Trinity and attempts to sit up but fails miserably. " What was that?"

Trinity looks at the door as if she is trying to see through with worry etched on her face for Neo. " I'm not sure.."

The lights flicker in the room and Neo starts to cough violently.

************************************************************************

" It's only a matter of time now before it all begins and they are once again back in this world to see the oracle."

One of the twins nod and say. " Are we to let them get to the oracle?"

Smith nods. " Yes. Keep away the agents that will most likely come and swarm them."

The twins nod and disappear into the night.

************************************************************************

His face red from coughing and with the help of Trinity sits up as the door bursts open. Morpheus and Tank enter the room and drag a helpless Neo away.

Trinity follows behind them. " Morpheus what's going on here?" 

" No time to explain now we need to get him out of here." Morpheus says as they enter the Neb. and take off leaving Zion behind.

Trinity sighs and looks at Morpheus. " All right we are out of Zion. Mind telling me what the rush was now Morpheus?" 

" The Sentinals were back. It's time to find the oracle Trinity. He has to see her and we can't delay it much longer and you know that."

" I know. I guess I'll go get him then." She turns and leaves to go get Neo. They both return a short time later.

Neo bites his lip as he sits in the chair waiting to be downloaded his face very pale.

" It's all right Neo." Trinity says right before they enter the Matrix. 

*********************************************************************

" They're in lets go." A twin tells his brother as they begin to stop most of the Agents, but two of them ends of getting past the twins. 

Neo, Trinity, and Morpheus enter the meeting spot to meet the oracle. The two agents appear suddenly from two passerby's in the street. 

Neo turns to face them. " Go!" He yells at Morpheus and Trinity. Morpheus nods solemnly and leaves with Trinity. They watch what's happening from the Neb. computer screens. Trinity stands next to Neo's chair. 

Knowing he wont be able to fight them for long because of the stupid virus he accepts the inevitable of what is going to happen moments before it does.

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Blood comes up from Neo's mouth in the real world and trinity wipes it away with a cloth. " They're killing him. I have to go in."

" Trinity no. He did this for us so we could escape he knew what was going to happen to himself." Morpheus tells her sternly. 

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The fight continues to rage on in the Matrix. It is evident Neo is getting warn out by the fight but continues on none the less. 

One of the agents grabs him and points a gun to his head.

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Trinity has tears in her eyes as she watches the screen from where she sat. " Neo! Please we need to help him.." 

Morpheus puts a hand on her shoulder. " He did what he had too Trinity..." He trails off as Neo's chair stops shaking and suddenly nothing at all happens. The line on the monitor above his chair beeps as it goes straight. 

Everyone in the room is silent expecting him to come back to life like he did before. After a few minutes of waiting his chair remains silent. Trinity stares at it with unbelieving eyes. " Neo..." she whispers quietly. 

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Smith bends down to check Neo's pulse and finds nothing. Satisfied at finally beating him he walks away. " Good Bye Mr. Anderson." 

A short while later Seraph comes acrosed Neo's body and drags it away to safety near the oracle were his body is gently laid on a bed. 

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Tank reaches a hand to unplug him but Trinity stops him. 

" Trinity he's gone. He's not coming back.." Tank says to her.

She shakes her head. " No. He may be gone now but I have a feeling he is going to come back. Please leave him Tank." She says stubbornly although she looks at him with pleading eyes. 

Tank sighs. " Fine." With that he walks away leaving Trinity alone.

" I don't know if you can hear me Neo... hang in there don't give up hope everything will be all right. I love you Neo." Trinity cries after she says this and walks into her room.

Morpheus stares at Neo disbelief shines in his eyes. " How can this be?" He quietly says to himself as he too finally walks away. 

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The Oracle stands over his body and watches him silently. Seraph watches her and asks her. " What does this mean?" 

The Oracle turns and looks at him. " He is between systems. He is neither here nor in the real world." 

" He's drifting? How is that possible?" Seraph asks her.

" The virus he seems to have obtained from somewhere is preventing him from coming back." The oracle answers. 

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It's been several months now since Neo has been gone, but his body still remains plugged into the chair in hopes that he will come back. Trinity sits next to the chair as they talk quietly about an up coming mission. 

" Alright so we go in and then what?" Trinity asks.

Morpheus sighs. " We find the contact and get the information from them." 

She nods as she walks over towards her chair and enters the matrix. 

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Trinity looks around at the various people. She stops suddenly as she sees someone that looks identical to Neo. 

Tank calls up Morpheus. " You wouldn't believe what's happening here."

" What is it Tank?" Morpheus asks.

" Trinity was right.." Tank cuts off the communication before it can be traced. 

Neo walks through the streets of the Matrix very confused. He sits down on a park bench and sighs. He knows he should remember something important about this place and about his past but he can't seem to get passed the mind block. It's as if someone erased all of his important memories. 

Trinity spots him and walks over to him. " Neo.." 

Neo looks up at hearing his name being called and stares at Trinity through blank eyes. " Trinity." The odd thing is he still seems to be able to remember people's names from what he calls his previous life. " I'm not who you think I am." He tells her quietly.

She looks at him with tears in her eyes and hugs him tightly. " Its alright Neo. I don't know what they've done to you, but we will fix it.. I promise you that." 

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They lay Neo down in a bed and look over him as he sleeps. Morpheus shakes his head.

" What is it Morpheus?" Trinity and the others ask.

" His memories have been tampered with. He still seems to remember us but nothing about this world or the Matrix."

Trinity runs a hand through his hair. " Is there anyway to bring them back?"

" I don't know Trinity. I don't think anything like this has happened before, but what we can do is start to retrain him.."

Trinity nods and sighs. " There has to be some way. When he wakes up I'll bring him out to the main deck to train.."

They nod and walk away from his room. Trinity stands in the corner of the room waiting for him to wake up. 

Neo wakes up a few hours later and Trinity leads him out to the main bridge. They have him sit in his chair and begin the training once again. 

Morpheus stands next to Neo after the combat training and after they fought. It seems that Neo is even faster than he was before. Morpheus jumps from the building top to building top with Neo following behind him in the jump program.

" This is amazing Tank." Trinity says to Tank as she watches them on the screen. 

Tank nods. " I know I've never seen anything like this before." 

One of the new crewmembers ask. " What does this mean?"

" It means he is the one, but we already knew that." Trinity sighs as she watches and what Neo told her the Oracle told him runs through her mind. ' You have the gift but it seems like you are waiting for something..' ' Could this what he was waiting for?' Trinity thinks to herself. 

Hours later Neo and Morpheus come out of the construct. Neo looks like he hardly broke a sweat in the training while Morpheus is sweating heavily.

Neo smiles brightly at Trinity as he comes out and walks over towards her. " Hey Trin." 

Trinity smiles back a bit sadly at Neo as she gives him a hug. " Do you remember anything at all Neo?" She asked although she knew that anyone was forbidden to talk to him about what happened.

His smile vanishes and he sighs. He closes his eyes trying to remember anything. " I- I remember a twilight dimension and then one morning I was here or there or whatever you want to call it." He says in frustration. 

She gives him a kiss. " It will be all right Neo. I promised that I would help you remember and that is a promise I intend to keep. You have given me a start just tell me if you remember anything more okay?"

He nods. " I will, and thanks Trinity I appreciate this."

******************************************************************

Smith scowls at the twins. " You had one simple job and you couldn't even take care of that!"

One of the twins looks at Smith and reply. " There were multiple agents there its not like there was only a few of them." His brother nods in agreement.

" I guess my lesson is learned. Never trust anyone else to do your work for you. If you want it done right do it yourself." Smith walks away to make new plans. He knows Neo is alive and knows that Neo is vulnerable. 

' This is the perfect time to strike them.' Smith thinks as he walks through the matrix. 

**********************************************************************

Neo walks through the ship and sits down in an empty chair in front of the matrix and sighs. It was rather late and he seemed to be the only person up. He stares blankly at the Matrix as it scrolls down the screen and sighs.

Trinity walks out of her room a short while later hearing someone else was up and walking down the hall. She walks quietly to the bridge and sits down next to him. " Can't sleep?"

He shakes his head. " No. I.." he trails off not knowing if what he was about to say would make any sense to her.

" You what Neo?" Trinity asks him softly.

" I can't make sense of this Trinity. I mean I have these memories of names but I can't remember a thing about these places or who I am and what I did in them.." 

Trinity looks at Neo and sighs wishing there was something she could say that could undo all that had been done to him. ' He doesn't deserve any of this' Trinity thinks as she sits there looking at him. She puts a hand on his arm. " Hang in there all right. We are going into the Matrix to see the oracle and ask her what can be done."

He shakes his head. " She doesn't know either."

" How do you know this Neo?" 

" That's who I was with when I woke up or whatever I did." 

" I wish there was something more we could do for you Neo. you don't deserve any of this." 

" Maybe I did." He says quietly. " Why else would it have happened?" He adds as an afterthought.

" No and you shouldn't think you did either. You of all people don't deserve this to happen to them. You've gone through so much already." 

Neo sighs wishing he could remember anything. He stands up and walks back towards the bedroom. 

Trinity sighs as she watches him leave. She stays up thinking for the remainder of the night.

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The next day Neo walks alone in the matrix. The crew abandons their duties and watches the matrix screen intently ready to get loaded into the matrix to help him out if needed.

Neo glances around the Matrix at the computer codes for a moment. He starts to walk again and glances around a bit nervously why he is nervous he doesn't know. 

" Mr. Anderson. I've been expecting you." Smith says as he steps out from the shadows. 

Neo turns and faces him. " What do you want?"

" I know what you seek. You seek answers to your questions about a life you don't remember. I have those answers."

Neo narrows his eyes not letting any surprise onto his face that Smith knew some of the reason why he was here. " And you want me to do what in return for those answers?"

" Predictable as always Mr. Anderson. Step out of the way. You don't know why you are fighting in this war how do you know that they just didn't take advantage of you." 

Neo shakes his head. " No they wouldn't do that. Trinity wouldn't let them." But a doubtful voice fills the back of his consciousness. ' But how do you really know that? How do you know that you should even be with them?' He shakes his head as if to clear away his thoughts and the voice vanishes.

Smith smirks at him. " I can see it in your eyes. You are confused and even now you wonder what you are doing here." 

**********************************************************************

Morpheus and Trinity enter the matrix and stand next to Neo. Morpheus glares coldly at Smith and trinity puts a hand on Neo's arm. " Neo don't listen to him.." 

" Morpheus we meet again." Smith says amused by this as if it was merely a game. 

Neo glances at Trinity and sighs. ' No. He's wrong this just somehow feels right.' he thinks and takes a step forward towards smith.

Smith raises an eyebrow and starts to attack him.

Neo even faster than the last time they fought easily bats the incoming fury of attacks aside and smiles. " You were saying?" He asks in a bored tone. 

" Impossible." Smith says as he attempts to fight off Neo. 

Trinity and Morpheus stand off to the side and smile. 

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Back at the ship however the people on board the Nebuchadnezzar was another story. Tank calls up Morpheus. " You need to get out of there now! Sentinals are everywhere." 

Morpheous sighs and drags Trinity towards an exit while Neo fights off Smith.

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The two of them come back into the real world and head to the cockpit. 

" What about Neo?" Trinity asks Morpheus.

" He'll make it. I know he will." 

The sentinals rip open the ship and one of them gets through It makes its way through the ship it goes straight to the bridge..

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Back in the Matrix The twins appear and join the fight. Smith smirks and disappears into the shadows.


	2. chapter 2

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Disclaimer: I do not own any characters you recognize in this story. I only own the plot and Sky. 

Neo faces them not really knowing what to expect from them but stands ready to fight none the less. He smiles feeling confident that he can beat them. " Bring it on."

One twin glides over behind Neo and starts to fight while his brother glides through Neo. It momentarily freezes his body and the twins use the extra time to their advantage. They brutally start to beat him.

Regaining his senses Neo parries the attacks and lands a few of his own. One of the twins go flying into a near by building.

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The lone sentinal continues its journey through the ship towards the bridge while the rest of the few other sentinals in its party remain outside as a distraction. Morpheus sits in the pilots chair waiting for the okay to use the emp.

Trinity runs towards the bridge. " How is he Tank?"

Tank watches the Matrix for a moment before responding to Trinity's question. " He has his hands full with these programs he is fighting. They are something new. I've never seen anything like them before."

Trinity bites her lip before she slowly asks. " Is he going to make it Tank?"

Tank sighs dreading to answer this question knowing how much both Trinity and Neo had gone through already. " I'm not going to lie to you Trinity.. I'm not sure if he will or not.."

Trinity sighs and walks back towards the cockpit and sits down in an empty chair.

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The battle rages one and neither side seems to be winning. The twins though seem to be linked together and move as one rather then two individual people. Neo flies back into a building.

Neo forces himself to get back up and takes out his phone.

One of the twins smirk and takes out a knife and destroys the phone. " Going somewhere?" The twin asks amused.

Neo Takes off running. The second twin glides in front of him. " We don't think so." The twin says with a smirk on his face.

Neo punches the twin but the punch hits nothing as the twin becomes transparent. The other twin comes from behind Neo and kicks him in the back.

Neo goes flying back landing in the opposite direction on his feet. He takes off running towards a person talking on their cell phone and grabs it out of their hand as he runs.

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"No!" Tank yells in frustration as Neo's signal in the matrix is suddenly gone.

Trinity runs towards the bridge hearing him yell. " What's going on?"

" His signal it just cut out. I can't find him anywhere."

Trinity looks over at his chair at the monitor above it and all his vitals seemed to be fine.

The sentinal breaks through and enters the bridge. It scans the bridge for a moment before going past them and heads towards Neo's chair. Its bright red laser beam starts to fire at Neo's body and Tank jumps in front of it.

Tank stands there for a moment before he falls down onto the deck dead.

Hearing all of this Morpheus turns on the EMP and blasts the sentinals.

The sentinal drowns down onto the deck millimeters away from his chair and Trinity screams knowing what happened. " Morpheus, He was still in there!" She yells frantically as Morpheus enters the bridge.

" I had to Trinity. I'm sorry.." Morpheus tells her as they both look at Neo.

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Neo staggers and collapses on the street. The twins look at one another and when they look back at the spot he collapsed his body is gone.

" We are confused."

" Yes we are." The second twin answers his brother as they vanish.

************************************************************************

For what seemed like an eternity Neo floats through a seemingly timeless dimension. He floats through it for sometime feeling very peaceful here. He dimly hears a voice. ' Neo please don't give up come back.' ' Trinity..' He thinks and he suddenly starts to fight his way back towards the bright lights of the real world.

TBC...

Reviewers:

Audrey A: Thank you. I'm glad your enjoying the story so far and that you like the plot.

Angel-Of-Lightness: I just was sitting in school one day bored out of my mind and I had just seen Reloaded and decided to write a matrix story and this is what came from it. Thanks for the rating.

Elenillor: Thanks I hope this chapter will be as enjoyable. 


	3. chapter 3

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Trinity looks down at the motionless Neo and the usual impassive look on her face is gone as a tear falls down her cheek. ' Neo please come back to me.' She takes a step back in shock when she sees that his eyes are open. She smiles down at him and takes his hand.

He looks up at her and looks around for a moment after she had unplugged him from the chair. His eyes light up with recognition and a bit of confusion as he looks back at her.

Trinity notices the look in his eyes and looks at him in question. " What is it Neo?" She asks him softly.

Remembering a few things about the real world he forgets a few details of his state of confusion and what happened in the matrix during then. " I just.." He starts not knowing exactly what to tell her. " Its nothing important it's just something I thought of."

Trinity looks at him with worry and concern on her face. She sighs. ' He can be so stubborn sometimes.' She thinks as she watches him.

" Really it's not important Trinity. It's just something I remembered. That's all." He says with a sigh.

Trinity sighs. " Please Neo.."

He sighs and says as he closes his eyes for a moment. " I remember pain lots of pain.. and some sort of machine inflicting it on me."

She raises her eyebrows. ' The Sentinal that inflicted him the virus..' she thinks as she looks at him and nods. ' The virus..' She thinks and clenches the fist that wasn't holding onto his hand.

" Are you all right Trinity?" He asks looking at her concerned as he gets out of the chair.

She smiles at him. ' No matter what happens to him he always worries about others first.' she thinks. " Yeah I was just thinking about something. It's not important." She adds seeing the look on his face.

He nods but sighs slightly not believing her. " If you say so." He says as he walks back towards the bedroom and goes to sleep.

She watches him for a moment and goes off to talk to Morpheus.

" What is it Trinity?" Morpheus asks concerned.

" He remembers about the virus.." She says simply.

Morpheus sighs. " The virus.. that's it." He says suddenly. 

What was it she didn't know as she watches him leave. She walks back towards the bedroom and enters it quietly watching Neo sleep for once peacefully. She sits down on one of the near by chairs and watches him for a moment and lets out a soft sigh. ' Why does everything seem to happen to him? He is always so strong so willing to make sacrifices so that others are spared, and now I must be willing to do the same for him.' She thinks as she watches him.

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Smith stares out of a window in a high building similar to the one Morpheus was kept at. ' The plan failed again.. There has to be a way. The virus.. of course that is the answer.' He turns away from the window and begins typing on a near by computer. As he works a smirk forms on his face.

******************************************************************

Neo's eyes snap open and he quickly sits up in the bed. He walks out of his room and glances around. He sits at an empty chair that was usually occupied by Tank and stares at the matrix and watches the green coding as it flows down the screen. He doesn't notice Trinity come out onto the deck and sit down next to him.

Trinity watches him silently as he stares into the flowing green waterfall of information that few understood. ' What is it that's bothering him?' She silently wonders as she sits there watching him.

He continues to sit there staring into the matrix thinking and jumps slightly when he noticed Trinity sitting there. " Hey" He says quietly to her.

" You okay Neo?" She asks concerned.

He nods. " Yeah I just can't sleep.."

She sighs and looks at him with piercing eyes that shine with concern and worry for him.

" It's another dream."

She shakes her head sadly. " You want to talk about it Neo?"

He hesitates for a moment before he finally nods. " Yeah sure." He finally says.

She sits there for a while in silence waiting for him to continue and she puts a hand on his arm gently comforting him.

" I know what the virus was meant to do know." He pauses seeing her about to say something but cuts her off as he continues. " It wasn't just made to get me like this. Something else is going on back in the Matrix. I think a new powerful program is getting made." He finishes and looks at her.

tbc..

A/N: One more chapter left in this story, but a sequel is in the process of being made. 


	4. chapter 4

#

#Disclaimer: See chapter one. 

After many hours of working Smith stands up from the desk and looks over at his creation of a new Rouge Program. With a few final minutes of typing the program awakes. " Go!" Smith commands the program.

The program codenamed Sky nods and with out a word takes off into the matrix.

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Trinity looks at him with a mixture of shock and horror on her face. She sits there watching him for a moment trying to find words to comfort him. She sighs quietly. 

" What's wrong Trinity?" He looks at her with a mixture of concern, compassion, and worry on his tired face.

Trinity manages to smile at him and pushes away her worried thoughts behind a wall that usually blocks her emotions from all others. " Nothing.. I was just thinking about something. You need to sleep."

He stands up and shakes his head. " I already told you I can't sleep.. More dreams will haunt my sleep and keep me awake, and besides its time to get up anyways. Soon we will be going into the Matrix."

She looks at him and stands up as well. " Neo no you can't go into the matrix like this. Especially with that Program running around. We don't know what it is capable of."

He sighs knowing she was going to say that. " Trinity listen.. Nothing is going to happen I won't let go. I have to go into the matrix and face this thing though."

Trinity sighs knowing he won't listen to reason since he set his mind to do this already. She walks after him as he starts to walk towards his chair.

" What are you doing?"

" What does it look like Neo? I'm going with you. You're going to need my help." Trinity tells him stubbornly.

Neo sighs knowing by now protesting with her when she has her mind set on doing something is a lost cause.

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They enter the matrix and shortly after Sky and Smith walk towards them. Sky at once heads towards Neo and begins the fight. Smith meanwhile was a mere distraction to Trinity to keep her away from interfering with the fight.

Neo fights for his life as he avoids punches and kicks from the program. A kick sends him flying back against the wall of a building.

The program walks over with an emotionless expression on its face and stands over Neo.

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Morpheus meanwhile was on board the Nebuchadnezzar working on a computer researching information that would help in solve the mystery. As he works every so often he glances at the Matrix. One of the crewmembers was acting as the operator since they didn't have a new one yet to replace Tank. Morpheus raises an eyebrow finally understanding what was going on. " Interesting..." he says to himself as he gazes over at the matrix.

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The fight meanwhile was definitely not going in Neo's favor. The program ruthlessly batted him around with ease. Sky grabs Neo and flies up into the air. He throws Neo down towards the ground.

Neo flies down to the ground at incredible speed. He watches the ground rush towards him helpless to do anything to prevent it. He hits the ground hard and moves no more.

Trinity breaks free of Smith's grip and runs towards him. She drags his body towards and exit and they soon leave.

Sky starts to follow them but Smith puts a hand out signaling him to stop. " There will be another time to finish the Job."  
Sky nods as Smith brings him back towards their base of operations.

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Massive bruises and a few broken bones were Neo's injuries. When he wakes up back in his in his bedroom on board the Nebechadnezzar Trinity and Morpheus are standing in his room. He looks up at them and smiles. His memory has been recovered and he had forgotten about the battle with the twins and about the Program. For now he just sits there resting from his injuries not knowing how he got them or he was even in a fight.

Trinity smiles back at him and says. " Get some rest I'll be back in a little while." She then walks out towards the mess hall to ensure that Neo won't hear her and Morpheus's conversation. She takes a seat at the table and waits for Morpheus to begin.

Morpheus looks at her as he sits down on the opposite side of the table from her. " The virus is the answer to all of the problems, and that is how that program was created. Sky as it's being called was made from the virus that had infected Neo. Every time he went into the matrix he suffered because of the virus. The virus took some of his coding and replicated it. The replication then got transferred to another computer until it was complete. Now that he has his memory back he won't remember the things that happened back inside the matrix during his state of confusion. Through the virus the program, Sky, and Neo are connected. He will remain with the virus until Sky is freed. He can't be destroyed, but since he has a human side to him know he can awaken and become a valuable ally to us in this war, but that will take time. No one can tell him other wise he must awaken on his own. When the time comes we must be ready for the other programs of the matrix will hunt him down."

Trinity stays silent through Morpheus's explanation. " What about his injuries?"

" Those will heal rapidly due to the strange connection since Sky was the one that did that damage." Morpheus gets up and walks away to brief the new operator, Link.

Trinity remains there at the table for a few moments before she walks back towards Neo's room. She sits down on the bed next to him and falls asleep shortly after.

Neo meanwhile drifts off into once again troubled sleep. He dreams about Trinity.

A/N: This is the last chapter in the story, but a sequel is in the process. Than you all to have reviewed and offered kind words in this story.

Reviewers:

Divamercury: Here is the final chapter of this story glad you liked the rest of the story.

Elenillor: Than you for the kind words. Here is the final chapter of the story.


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